In this paper, a hierarchical validation procedure for validation of the simulated high-intensity radiated field (HIRF) effects in electromagnetic (EM) models are established. A three-stage process of EM model hierarchical validation (from the bottom up) is proposed: unit stage, benchmark stage, and system stage. A rectangular enclosure benchmark model, a metallic case model with multiple slots and apertures, and a real aircraft model have been used in this paper. For each stage, numerical results have been compared to measurements with the implementation of the uncertainty quantification (UQ) and validation metric. The proposed hierarchical validation methodology has been applied in the validation of the real aircraft model under HIRF conditions. The framework presented here is also appropriate for the other real structures, which can offer valuable insight for both protection design as well as optimization and electromagnetic compatibility.